For wood, the cheapest is to collect and process your own wood. I don't have all that much "beautiful" wood for pens around me, so I find that the vendors here on IAP provide the nicest variety of blanks at the best prices. I'd make it a point to check out the vendor offerings each time I came to the site.
For pen components, first decide which brand and type of kits you most desire. Again, the IAP vendors often have discounts so keep your eyes open. The February Bash is a great time to shop. The group purchases also offer great deals, particularly if you need stuff from Craft Supply USA. You have to keep checking because they fill up rapidly. For some reason, even though I'm subscribed to the Group Purchases forum, I'm never notified of a new thread until a week or so after the fact and usually after the buy group has filled.
All the vendors in the "Vendor Cheers" forum are great to shop around in. My problem is I have way too much fun buying things and find myself with a huge parts inventory. I need to get downstairs and start making pens!